That's the problem, it has been disabled since the beginning and is still disabled and is also disabled in litespeed. How can it enable itself by default when it is both disabled in cPanel and litespeed ?

I haven't checked the apache files to see if it's an issue with cPanel or litespeed. Updating litespeed + php with easy apache also updated Apache so this could be a cPanel bug, but this would be a first for cPanel's easy apache.

We are running cPanel's stable release branch so we are currently running version 11.36.1 build 8 with the latest version of easy apache.

if it shows 'Indexes default' in the 'Global Configuration' but yours is unchecked, likely someone changed after install because 'default' indicates Indexes is supposed to be checked/enabled by default.

There was an issue with the mail.local template that kept some things from a previous version of easyapache that is shouldn't have. Reverting to the up to date default apache template solved the issue that was making an apache rebuild fail and building with default settings.